I: pbuilder: network access will be disabled during build
I: Current time: Sun Mar 9 07:16:57 +14 2025
I: pbuilder-time-stamp: 1741454217
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [codonw_1.4.4-8.dsc]
I: copying [./codonw_1.4.4.orig.tar.gz]
I: copying [./codonw_1.4.4-8.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./codonw_1.4.4-8.dsc: unsupported subcommand
dpkg-source: info: extracting codonw in codonw-1.4.4
dpkg-source: info: unpacking codonw_1.4.4.orig.tar.gz
dpkg-source: info: unpacking codonw_1.4.4-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening
dpkg-source: info: applying enable_clean
dpkg-source: info: applying remove_pause
dpkg-source: info: applying define_linux
dpkg-source: info: applying spelling
dpkg-source: info: applying helpfile_location
dpkg-source: info: applying fix_link_name_clashes
dpkg-source: info: applying remove_nondeterminism
dpkg-source: info: applying remove-gets.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/D01_modify_environment starting
debug: Running on ionos2-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Mar 8 17:17 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
DIRSTACK=()
DISTRIBUTION=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=5303521dc1dd400988c2c58e385b9a1b
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=6203
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.29sh9YfU/pbuilderrc_RTXc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.29sh9YfU/b2 --logfile b2/build.log codonw_1.4.4-8.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://46.16.76.132:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19787 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.8 MB of archives. After unpacking 78.2 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-7 [301 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Fetched 20.8 MB in 0s (68.0 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
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(Reading database ... 100%
(Reading database ... 19787 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.23.1-1_i386.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-5_i386.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-7_i386.deb ...
Unpacking m4 (1.4.19-7) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-3_all.deb ...
Unpacking libtool (2.5.4-3) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:i386.
Preparing to unpack .../21-libelf1t64_0.192-4_i386.deb ...
Unpacking libelf1t64:i386 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_i386.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:i386.
Preparing to unpack .../23-libunistring5_1.3-1_i386.deb ...
Unpacking libunistring5:i386 (1.3-1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../24-libicu72_72.1-6_i386.deb ...
Unpacking libicu72:i386 (72.1-6) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_i386.deb ...
Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.23.1-1_i386.deb ...
Unpacking gettext (0.23.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libicu72:i386 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-7) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:i386 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/codonw-1.4.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../codonw_1.4.4-8_source.changes
dpkg-buildpackage: info: source package codonw
dpkg-buildpackage: info: source version 1.4.4-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4'
rm -rf *.o *.coa *.blk *.out *raw codonw codonW.log
make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4'
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4'
rm -rf debian/man
dh_clean --exclude=Makefile.orig
make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j10 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4'
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codon_us.c
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codons.c
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 open_fil.c
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 commline.c
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 menu.c
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 tester.c
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c
codon_us.c: In function 'codon_usage_out':
codon_us.c:373:24: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
373 | fprintf(fblkout, "%i%c",nncod[x],sp);
| ~^ ~~~~~~~~
| | |
| int long int
| %li
codon_us.c: In function 'raau_usage_out':
codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args]
479 | fprintf(fblkout, "\n",sp);
| ^~~~
codon_us.c: In function 'cbi_out':
codon_us.c:831:32: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=]
831 | sprintf(pm->messages, " Serious error in CBI information found"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
836 | pcbi->fop_cod[x], x);
| ~~~~~~~~~~~~~~~~
| |
| int
codon_us.c:832:38: note: format string is defined here
832 | " an illegal CBI value of %f for codon %i"
| ~^
| |
| double
| %d
codon_us.c: In function 'fop_out':
codon_us.c:988:28: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=]
988 | sprintf(pm->messages, " Serious error in fop information found"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
993 | pfop->fop_cod[x], x);
| ~~~~~~~~~~~~~~~~
| |
| int
codon_us.c:989:37: note: format string is defined here
989 | " an illegal fop value of %f for codon %l"
| ~^
| |
| double
| %d
codon_us.c:988:28: warning: unknown conversion type character ' ' in format [-Wformat=]
988 | sprintf(pm->messages, " Serious error in fop information found"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c:990:11: note: format string is defined here
990 | " permissible values are \n 1 for non-optimal"
| ^
codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args]
988 | sprintf(pm->messages, " Serious error in fop information found"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c:994:25: warning: unknown conversion type character ',' in format [-Wformat=]
994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt);
| ^
codon_us.c:994:33: warning: unknown conversion type character ',' in format [-Wformat=]
994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt);
| ^
codon_us.c:994:44: warning: unknown conversion type character '\x0a' in format [-Wformat=]
994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt);
| ^~
codon_us.c:994:18: warning: too many arguments for format [-Wformat-extra-args]
994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c: In function 'gc_out':
codon_us.c:1181:10: warning: too many arguments for format [-Wformat-extra-args]
1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c: In function 'dinuc_out':
codon_us.c:1476:39: warning: precision used with '%c' gnu_printf format [-Wformat=]
1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp);
| ^
codon_us.c: In function 'hydro_out':
open_fil.c: In function 'open_file':
open_fil.c:88:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
open_fil.c:133:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
133 | fgets(answer, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
166 | fgets(temp, 3, stdin);
| ^~~~~~~~~~~~~~~~~~~~~
open_fil.c:186:21: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
186 | fgets(answer, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c: In function 'main':
codons.c:190:55: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
190 | fprintf(pm->my_err,"\n\n\t\tNumber of sequences: %i\n",
| ~^
| |
| int
| %li
191 | num_sequence);
| ~~~~~~~~~~~~
| |
| long int
codons.c:196:32: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
196 | fprintf(pm->my_err, "\tWARNING\t At least one sequence in your"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
197 | " input file has\ninternal stop codons (found %i"
198 | " internal stops) \tWARNING\n",num_seq_int_stop);
| ~~~~~~~~~~~~~~~~
| |
| long int
codons.c:197:68: note: format string is defined here
197 | " input file has\ninternal stop codons (found %i"
| ~^
| |
| int
| %li
codons.c:200:46: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal "
| ~^
| |
| int
| %li
201 | "stop codons \tWARNING\n",num_seq_int_stop);
| ~~~~~~~~~~~~~~~~
| |
| long int
open_fil.c:88:13: warning: 'fgets' writing 8192 bytes into a region of size 90 overflows the destination [-Wstringop-overflow=]
88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
open_fil.c:71:12: note: destination object 'infile_name' of size 90
71 | char infile_name[MAX_FILENAME_LEN]="";
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:970,
from open_fil.c:47:
/usr/include/i386-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n,
| ^~~~~
codon_us.c:2115:27: warning: too many arguments for format [-Wformat-extra-args]
2115 | fprintf(pm->my_err, "No output was written to file \n", title);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c: In function 'aromo_out':
codon_us.c:2148:27: warning: too many arguments for format [-Wformat-extra-args]
2148 | fprintf(pm->my_err, "No output was written to file \n", title);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c: In function 'toutput':
In file included from codon_us.c:77:
codon_us.c: In function 'codon_error':
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c:347:6: note: in expansion of macro 'pause'
347 | pause;
| ^~~~~
codons.c:640:25: warning: unknown conversion type character '=' in format [-Wformat=]
640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:641:11: note: format string is defined here
641 | " =%5.3f\n" /* with G+C content and length of gene */
| ^
codons.c:647:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters "
| ~^
| |
| int
| %ld
648 | "in sequence %i\n"
649 | ,non_std_char - IUBC_TOT
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long int
codons.c:647:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
650 | ,num_sequence);
| ~~~~~~~~~~~~
| |
| long int
codon_us.c: In function 'cai_out':
codon_us.c:652:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
652 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:648:25: note: format string is defined here
648 | "in sequence %i\n"
| ~^
| |
| int
| %li
codon_us.c: In function 'cbi_out':
codon_us.c:759:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
759 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:652:30: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
652 | fprintf(pm->my_err, "\t%3i>\t%6li %-40.40s\tPROTEIN\n"
| ~~^
| |
| int
| %3li
653 | ,num_sequence
| ~~~~~~~~~~~~
| |
| long int
codons.c:657:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
657 | fprintf(pm->my_err, "\t\t WARNING %d non "
| ~^
| |
| int
| %ld
......
660 | ,non_std_char
| ~~~~~~~~~~~~
| |
| long int
codon_us.c: In function 'fop_out':
codon_us.c:899:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
899 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:657:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
657 | fprintf(pm->my_err, "\t\t WARNING %d non "
| ^~~~~~~~~~~~~~~~~~~~~~
......
661 | ,num_sequence);
| ~~~~~~~~~~~~
| |
| long int
codon_us.c:957:14: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
957 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:659:25: note: format string is defined here
659 | "in sequence %i\n"
| ~^
| |
| int
| %li
codons.c: In function 'output':
codons.c:800:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
800 | fprintf(stderr, "ERROR-23 %s bulk undefined\n", pm->prog);
| ~^ ~~~~~~~~
| | |
| char * int
| %d
codons.c:805:32: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
805 | fprintf(stderr, "ERROR-24 %s -prog undefined\n", pm->prog);
| ~^ ~~~~~~~~
| | |
| char * int
| %d
codon_us.c: In function 'gen_cusort_fop':
codon_us.c:1699:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c:1700:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
codon_us.c:1703:8: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 */
| ^~~~~~~~~~~~~~~~~~~~~~~
codon_us.c:1711:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in */
| ^~~~~~~~~~~~~~~~~~~~~~~~~
tester.c: In function 'tester':
tester.c:88:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
88 | fgets( pm->junk , BUFSIZ, stdin) ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tester.c:125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
125 | fgets( pm->junk , BUFSIZ, stdin) ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tester.c:170:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
170 | fgets( pm->junk , BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from codons.c:90:
codons.c: In function 'main':
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:204:35: note: in expansion of macro 'pause'
204 | if ( pm->codonW && pm->menu ) pause;
| ^~~~~
In file included from commline.c:28:
commline.c: In function 'proc_comm_line':
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
commline.c:103:9: note: in expansion of macro 'pause'
103 | pause;
| ^~~~~
In file included from tester.c:48:
tester.c: In function 'asummary':
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
commline.c:127:9: note: in expansion of macro 'pause'
127 | pause;
| ^~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
commline.c:142:9: note: in expansion of macro 'pause'
142 | pause;
| ^~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tester.c:235:5: note: in expansion of macro 'pause'
235 | pause;
| ^~~~~
In file included from menu.c:31:
menu.c: In function 'main_menu':
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:69:9: note: in expansion of macro 'pause'
69 | pause;
| ^~~~~
menu.c: In function 'menu_initial':
menu.c:106:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
106 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:122:29: note: in expansion of macro 'pause'
122 | pause;
| ^~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:132:17: note: in expansion of macro 'pause'
132 | pause;
| ^~~~~
menu.c: In function 'menu_2':
menu.c:233:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
233 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:250:17: note: in expansion of macro 'pause'
250 | pause;
| ^~~~~
codons.c: In function 'chelp':
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:1078:20: note: in expansion of macro 'pause'
1078 | pause; /* make sure they Ack. the error mesg */
| ^~~~~
menu.c: In function 'menu_3':
menu.c:305:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
305 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:322:17: note: in expansion of macro 'pause'
322 | pause;
| ^~~~~
menu.c:345:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
345 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:382:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
382 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:401:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
401 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:425:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
425 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:450:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
450 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c: In function 'menu_4':
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:1097:35: note: in expansion of macro 'pause'
1097 | if ( line_counter )pause;
| ^~~~~
menu.c:580:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
580 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:620:17: note: in expansion of macro 'pause'
620 | pause;
| ^~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:640:17: note: in expansion of macro 'pause'
640 | pause;
| ^~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:660:17: note: in expansion of macro 'pause'
660 | pause;
| ^~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:1115:5: note: in expansion of macro 'pause'
1115 | pause;
| ^~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:1124:4: note: in expansion of macro 'pause'
1124 | pause;
| ^~~~~
menu.c: In function 'menu_5':
menu.c:764:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
764 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:814:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
814 | fgets( pm->junk , BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codons.c:1128:5: note: in expansion of macro 'pause'
1128 | pause;
| ^~~~~
menu.c: In function 'menu_6':
menu.c:844:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
844 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:861:17: note: in expansion of macro 'pause'
861 | pause;
| ^~~~~
menu.c: In function 'menu_7':
menu.c:893:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
893 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:912:17: note: in expansion of macro 'pause'
912 | pause;
| ^~~~~
menu.c: In function 'menu_8':
menu.c:975:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
975 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:1007:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1007 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:1024:11: note: in expansion of macro 'pause'
1024 | pause;
| ^~~~~
menu.c: In function 'menu_coa':
menu.c:1067:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1067 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:1085:9: note: in expansion of macro 'pause'
1085 | pause;
| ^~~~~
menu.c:1097:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1097 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:1117:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1117 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c:1130:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1130 | fgets ( pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
menu.c: In function 'select_coa':
menu.c:1224:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1224 | fgets(pm->junk, BUFSIZ, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c: In function 'textbin':
coresp.c:98:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
98 | fscanf(pm->fcoa_in,"%s",pm->junk);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c:104:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
104 | fscanf(pm->fcoa_in,"%i",&v2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c:108:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
108 | fscanf(pm->fcoa_in,"%i\n",&v2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c:115:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
115 | fscanf(pm->fcoa_in,"%i",&v2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c:119:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | fscanf(pm->fcoa_in,"%i\n",&v2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c:127:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
127 | fscanf(pm->fcoa_in,"%i",&v2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c:131:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
131 | fscanf(pm->fcoa_in,"%i\n",&v2); /* read last codon */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c: In function 'rowout':
coresp.c:277:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
277 | fgets(pm->junk,BUFSIZ,fnam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'fgets',
inlined from 'open_file' at open_fil.c:88:13:
/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c: In function 'inertialig':
coresp.c:1271:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1271 | fgets(pm->junk,BUFSIZ,fnam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c:1315:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1315 | fgets(pm->junk,BUFSIZ,fnam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
coresp.c: In function 'suprow':
coresp.c:1619:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1619 | fgets(pm->junk,BUFSIZ,fnam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=]
620 | printf("Could not open input file - %s\n", p );
| ^~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wl,-z,relro -Wl,-z,now codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o -o codonw -lm
make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4'
mkdir -p debian/codonw/usr/bin
cp codonw debian/codonw/usr/bin
mkdir -p debian/codonw/usr/share/codonw
cp codonW.hlp debian/codonw/usr/share/codonw
chmod -x debian/codonw/usr/share/codonw/codonW.hlp
make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4'
dh_install
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4'
mkdir -p debian/codonw/usr/share/doc/codonw
cp *.txt debian/codonw/usr/share/doc/codonw
dh_installdocs --
make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4'
dh_installchangelogs
dh_installexamples
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4'
mkdir -p /build/reproducible-path/codonw-1.4.4/debian/man
/build/reproducible-path/codonw-1.4.4/debian/make_man.pl /build/reproducible-path/codonw-1.4.4/debian/template.man \
/build/reproducible-path/codonw-1.4.4/debian/man
calculate Effective Number of Codons (ENc)
calculate Frequency of OPtimal codons index (FOP)
calculate Relative Amino Acid Usage (RAAU)
calculate Relative Synonymous Codon Usage (RSCU)
output sequence in reader format
G+C content of gene (all 3 codon positions)
calculate Codon Bias Index (CBI)
calculate Amino Acid Usage (AAU)
GC of synonymous codons 3rd positions
calculate Codon Adaptation Index (CAI)
tabulation of codon usage
calculate codon usage
silent base G+C+A+T calculating program
clean up sequence in FASTA format
conceptual translation of DNA to amino acid
tabulation of datasets codon usage
dinucleotide usage of the three codon positions
detailed report of base composition
dh_installman --
make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4'
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4'
dh_fixperms
chmod -x debian/codonw/usr/share/doc/codonw/examples/input.dat
make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4'
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'codonw' in '../codonw_1.4.4-8_i386.deb'.
dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_i386.deb'.
dpkg-genbuildinfo --build=binary -O../codonw_1.4.4-8_i386.buildinfo
dpkg-genchanges --build=binary -O../codonw_1.4.4-8_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/6203/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/6203 and its subdirectories
I: Current time: Sun Mar 9 07:18:01 +14 2025
I: pbuilder-time-stamp: 1741454281